... | ... |
@@ -5,27 +5,24 @@ |
5 | 5 |
\title{Function to visualize cell-level information on segmentation masks} |
6 | 6 |
\usage{ |
7 | 7 |
plotCells( |
8 |
- object, |
|
9 | 8 |
mask, |
10 |
- cell_id, |
|
11 |
- img_id, |
|
9 |
+ object = NULL, |
|
10 |
+ cell_id = NULL, |
|
11 |
+ img_id = NULL, |
|
12 | 12 |
colour_by = NULL, |
13 | 13 |
outline_by = NULL, |
14 | 14 |
exprs_values = "counts", |
15 | 15 |
subset_images = NULL, |
16 | 16 |
colour = NULL, |
17 |
- missing_colour = "gray", |
|
18 |
- scale_bar = list(length = 20, label = NULL, cex = 1, lwd = 2, colour = "white", margin = c(10,10)), |
|
19 |
- image_title = list(text = NULL, position = "top", cex = 1, colour = "white", margin = 10, font = 2), |
|
20 | 17 |
... |
21 | 18 |
) |
22 | 19 |
} |
23 | 20 |
\arguments{ |
24 |
-\item{object}{a \code{\linkS4class{SingleCellExperiment}} object.} |
|
25 |
- |
|
26 | 21 |
\item{mask}{an \code{\linkS4class{ImageList}} object single-channel |
27 | 22 |
\code{\linkS4class{Image}} objects (see Details)} |
28 | 23 |
|
24 |
+\item{object}{a \code{\linkS4class{SingleCellExperiment}} object.} |
|
25 |
+ |
|
29 | 26 |
\item{cell_id}{character specifying the \code{colData(object)}, in which the |
30 | 27 |
integer cell IDs are stored} |
31 | 28 |
|
... | ... |
@@ -41,11 +38,7 @@ integer cell IDs are stored} |
41 | 38 |
|
42 | 39 |
\item{colour}{TODO} |
43 | 40 |
|
44 |
-\item{missing_colour}{TODO} |
|
45 |
- |
|
46 |
-\item{scale_bar}{TODO} |
|
47 |
- |
|
48 |
-\item{...}{TODO} |
|
41 |
+\item{...}{Further arguments passed to \code{?"\link{plotting-param}"}} |
|
49 | 42 |
} |
50 | 43 |
\value{ |
51 | 44 |
TODO |
... | ... |
@@ -11,12 +11,10 @@ plotPixels( |
11 | 11 |
cell_id = NULL, |
12 | 12 |
img_id = NULL, |
13 | 13 |
colour_by = NULL, |
14 |
+ bcg = NULL, |
|
14 | 15 |
outline_by = NULL, |
15 | 16 |
subset_images = NULL, |
16 | 17 |
colour = NULL, |
17 |
- missing_colour = "gray", |
|
18 |
- scale_bar = list(length = 20, label = NULL, cex = 1, lwd = 2, colour = "white", margin = c(10,10)), |
|
19 |
- image_title = list(text = NULL, position = "top", cex = 1, colour = "white", margin = 10, font = 2), |
|
20 | 18 |
... |
21 | 19 |
) |
22 | 20 |
} |
... | ... |
@@ -36,17 +34,15 @@ integer cell IDs are stored} |
36 | 34 |
|
37 | 35 |
\item{colour_by}{TODO} |
38 | 36 |
|
37 |
+\item{bcg}{brightness/contrast/gamma list("H3" = c(0,1,1))} |
|
38 |
+ |
|
39 | 39 |
\item{outline_by}{(optional)} |
40 | 40 |
|
41 |
-\item{subset_images}{TODO} |
|
41 |
+\item{subset_images}{TODO Note that Masks and Images need to have same names or same IDs} |
|
42 | 42 |
|
43 | 43 |
\item{colour}{TODO} |
44 | 44 |
|
45 |
-\item{missing_colour}{TODO} |
|
46 |
- |
|
47 |
-\item{scale_bar}{TODO} |
|
48 |
- |
|
49 |
-\item{...}{TODO} |
|
45 |
+\item{...}{Further arguments passed to \code{?"\link{plotting-param}"}} |
|
50 | 46 |
} |
51 | 47 |
\value{ |
52 | 48 |
TODO |
... | ... |
@@ -4,17 +4,11 @@ |
4 | 4 |
\alias{plotting-param} |
5 | 5 |
\title{Further plotting parameters for the SingleCellMapper package} |
6 | 6 |
\arguments{ |
7 |
-\item{legend_size}{TODO} |
|
7 |
+\item{missing_colour}{TODO} |
|
8 | 8 |
|
9 |
-\item{title_size}{TODO} |
|
9 |
+\item{scale_bar}{TODO} |
|
10 | 10 |
|
11 |
-\item{title_colour}{TODO} |
|
12 |
- |
|
13 |
-\item{return_plot}{TODO} |
|
14 |
- |
|
15 |
-\item{return_images}{TODO} |
|
16 |
- |
|
17 |
-\item{save_images}{TODO} |
|
11 |
+\item{image_title}{TODO} |
|
18 | 12 |
} |
19 | 13 |
\value{ |
20 | 14 |
TODO |
... | ... |
@@ -25,6 +19,10 @@ TODO |
25 | 19 |
\section{Setting further parameters}{ |
26 | 20 |
|
27 | 21 |
TODO |
22 |
+# legend list(title, size) also allow NULL |
|
23 |
+# return_plot TODO |
|
24 |
+# return_images TODO |
|
25 |
+# save_images TODO |
|
28 | 26 |
} |
29 | 27 |
|
30 | 28 |
\examples{ |
... | ... |
@@ -197,6 +197,7 @@ test_that("plotPixels: Cells can be outlined correctly.", { |
197 | 197 |
test_that("plotPixels: images can be correctly subsetted.", { |
198 | 198 |
data("pancreasSCE") |
199 | 199 |
data("pancreasMasks") |
200 |
+ data("pancreasImages") |
|
200 | 201 |
|
201 | 202 |
# Works |
202 | 203 |
expect_silent(plotPixels(image = pancreasImages, |
... | ... |
@@ -230,7 +231,7 @@ test_that("plotPixels: images can be correctly subsetted.", { |
230 | 231 |
expect_silent(plotPixels(image = pancreasImages, |
231 | 232 |
mask = pancreasMasks, |
232 | 233 |
object = pancreasSCE, |
233 |
- img_id = "ImageName", |
|
234 |
+ img_id = "ImageNb", |
|
234 | 235 |
cell_id = "CellNb", |
235 | 236 |
colour_by = "SMA", |
236 | 237 |
outline_by = "CellType", |
... | ... |
@@ -367,7 +368,7 @@ test_that("plotPixels: Size of images can be changed.", { |
367 | 368 |
# Decreasing the size |
368 | 369 |
cur_masks <- pancreasMasks |
369 | 370 |
setImages(cur_masks, "A02_mask") <- cur_masks[[1]][1:50, 1:50,,drop=FALSE] |
370 |
- expect_error(plotPixels(object = cur_sce, |
|
371 |
+ expect_error(plotPixels(object = pancreasSCE, |
|
371 | 372 |
image = pancreasImages, |
372 | 373 |
mask = cur_masks, img_id = "ImageNb", |
373 | 374 |
cell_id = "CellNb", |
... | ... |
@@ -379,12 +380,12 @@ test_that("plotPixels: Size of images can be changed.", { |
379 | 380 |
cur_images <- pancreasImages |
380 | 381 |
setImages(cur_images, "A02_imc") <- cur_images[[1]][1:50, 1:50,,drop=FALSE] |
381 | 382 |
|
382 |
- expect_silent(plotPixels(object = cur_sce, |
|
383 |
+ expect_silent(plotPixels(object = pancreasSCE, |
|
383 | 384 |
image = cur_images, |
384 | 385 |
mask = cur_masks, img_id = "ImageNb", |
385 | 386 |
cell_id = "CellNb", |
386 | 387 |
colour_by = "H3", outline_by = "CellType")) |
387 |
- expect_silent(plotPixels(object = cur_sce, |
|
388 |
+ expect_silent(plotPixels(object = pancreasSCE, |
|
388 | 389 |
image = cur_images, |
389 | 390 |
mask = cur_masks, img_id = "ImageNb", |
390 | 391 |
cell_id = "CellNb", |